comparison mqparam.py @ 3:175e062b6a17 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"

2:666f3453a99d

        True
        """

        child = ET.SubElement(el, name, attrib=attrib if attrib else {})
        child.text = str(text)

    def _make_exp_design(self, infiles):
        """Create a dict representing an experimental design from
        an experimental design template and a list of input files.
        If the experimental design template is None, create a default

        >>> design['Name']
        ['./test-data/BSA_min_21.mzXML', './test-data/BSA_min_22.mzXML']
        >>> design['Fraction']
        ['1', '2']
        """
        design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment")}
        if not self.exp_design:
            design["Name"] = infiles
            design["Fraction"] = ('32767',) * len(infiles)
            design["Experiment"] = [os.path.split(f)[1] for f in infiles]

                index = []
                for i in index_line.split('\t'):
                    if i in design:
                        index.append(i)
                    else:
                        raise Exception("Invalid comlumn index in experimental"
                                        + " design template: {}".format(i))
                for line in design_file:
                    row = line.strip().split('\t')
                    for e, i in zip_longest(row, index):
                        design[i].append(e)

            # map infiles to names in exp. design template
            names = []
            names_to_paths = {}

                fname = re.sub(self.substitution_rx, '_', name)
                names.append(names_to_paths[fname] if fname in names_to_paths
                             else None)
            # replace orig. file names with matching links to galaxy datasets
            design['Name'] = names

        return design

    def add_infiles(self, infiles, interactive):
        """Add a list of raw/mzxml files to the mqpar.xml.

        fasta_node.clear()
        fasta_node.tag = "fastaFiles"

        for index in range(len(files)):
            filepath = '<fastaFilePath>' + files[index]
            fasta = self.fasta_template.replace('<fastaFilePath>', filepath)
            fasta = fasta.replace('<identifierParseRule>',
                                  '<identifierParseRule>' + identifier)
            fasta = fasta.replace('<descriptionParseRule>',
                                  '<descriptionParseRule>' + description)

3:175e062b6a17

        True
        """

        child = ET.SubElement(el, name, attrib=attrib if attrib else {})
        child.text = str(text)

    @staticmethod
    def _check_validity(design, len_infiles):
        "Perform some checks on the exp. design template"
        design_len = len(design['Name'])
        match = len(list(filter(lambda x: bool(x), design['Name'])))
        if match < len_infiles:
            raise Exception("Error parsing experimental design template: " +
                            "Found only {} matching entries ".format(design_len) +
                            "for {} input files".format(len_infiles))
        for i in range(0, design_len):
            msg = "Error in line " + str(i + 2) + " of experimental design: "
            if not (design['Name'][i] and design['Experiment'][i]):
                raise Exception(msg + " Name or Experiment is empty.")
            if design['PTM'][i].lower() not in ('true', 'false'):
                raise Exception(msg + "Defines invalid PTM value, " +
                                "should be 'True' or 'False'.")
            try:
                int(design['Fraction'][i])
            except ValueError as e:
                raise Exception(msg + str(e))

    def _make_exp_design(self, infiles):
        """Create a dict representing an experimental design from
        an experimental design template and a list of input files.
        If the experimental design template is None, create a default

        >>> design['Name']
        ['./test-data/BSA_min_21.mzXML', './test-data/BSA_min_22.mzXML']
        >>> design['Fraction']
        ['1', '2']
        """

        design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment")}
        if not self.exp_design:
            design["Name"] = infiles
            design["Fraction"] = ('32767',) * len(infiles)
            design["Experiment"] = [os.path.split(f)[1] for f in infiles]

                index = []
                for i in index_line.split('\t'):
                    if i in design:
                        index.append(i)
                    else:
                        raise Exception("Invalid column index in experimental"
                                        + " design template: {}".format(i))

                for line in design_file:
                    row = line.strip().split('\t')
                    for e, i in zip_longest(row, index):
                        if i == "Fraction" and e == '':
                            e = 32767
                        elif i == "PTM" and not e:
                            e = 'False'
                        design[i].append(e)

            # map infiles to names in exp. design template
            names = []
            names_to_paths = {}

                fname = re.sub(self.substitution_rx, '_', name)
                names.append(names_to_paths[fname] if fname in names_to_paths
                             else None)
            # replace orig. file names with matching links to galaxy datasets
            design['Name'] = names
            MQParam._check_validity(design, len(infiles))

        return design

    def add_infiles(self, infiles, interactive):
        """Add a list of raw/mzxml files to the mqpar.xml.

        fasta_node.clear()
        fasta_node.tag = "fastaFiles"

        for index in range(len(files)):
            filepath = '<fastaFilePath>' + files[index]
            identifier = identifier.replace('<', '&lt;')
            description = description.replace('<', '&lt;')
            fasta = self.fasta_template.replace('<fastaFilePath>', filepath)
            fasta = fasta.replace('<identifierParseRule>',
                                  '<identifierParseRule>' + identifier)
            fasta = fasta.replace('<descriptionParseRule>',
                                  '<descriptionParseRule>' + description)